Expression analysis of global gene response to chronic heat exposure in broiler chickens (Gallus gallus) reveals new reactive genes

RNA-seq reveals changes in the transcriptome of the breast muscle of adult female chickens in response to heat stress

BACKGROUND

Heat stress has caused significant impacts on the poultry industry globally. Tianjin-monkey Chicken (TM) is a local naked neck chicken genetic resource in China, characterized by its heat stress resistance due to a low feather coverage.

RESULTS

We conducted heat stress stimulation tests on TM and a normal feathered chicken (Jingfen No. 6 Layer, JF), and the breast muscle tissues were collected for transcriptome sequencing. A total of 157 differentially expressed genes (DEGs) and 1435 DEGs were respectively obtained from the comparisons of JFN-vs-JFT and TMN-vs-TMT. GO enrichment analysis found that biological process (BP) terms including phospholipid homeostasis, regulation of aggrephagy, positive regulation of aggrephagy, and negative regulation of lipase activity may be closely related to heat stress resistance in JF chickens. While catabolism-related BP terms were mainly enriched for DEGs of TM, such as catabolic process, protein catabolic process and cellular catabolic process. KEGG pathway analysis showed that the MAPK signaling pathway was enriched both in TM and JF with high connectivity. In addition, some pathways with higher connectivity (Metabolic pathways, FoxO signaling pathway, TGF-beta signaling pathway and AMPK signaling pathway) may be closely associated with resistance to heat stress in JF. In Tianjin-monkey Chicken, we also identified several pathways potentially involved in heat stress regulation, including Ubiquitin mediated proteolysis, Autophagy-animal and Regulation of actin cytoskeleton. Protein-Protein Interaction Networks (PPI) for the 24 co-differentially expressed genes revealed four key genes (Klf9, Asb2, Tmem164 and Arrdc2) associated with heat stress both in JF and TM.

CONCLUSIONS

Our findings will enrich the research on heat stress resistance in chicken skeletal muscle, while also providing a theoretical basis for the genetic improvement of heat stress resistance in chickens.

Investigating the potential role of the pituitary adenylate cyclase-activating polypeptide (PACAP) in regulating the ubiquitin signaling pathway in poultry

The physiological processes in animal production are regulated through biologically active molecules like peptides, proteins, and hormones identified through the development of the fundamental sciences and their application. One of the main polypeptides that plays an essential role in regulating physiological responses is the pituitary adenylate cyclase-activating polypeptide (PACAP). PACAP belongs to the glucagon/growth hormone-releasing hormone (GHRH)/vasoactive intestinal proteins (VIP) family and regulates feed intake, stress, and immune response in birds. Most of these regulations occur after PACAP stimulates the cAMP signaling pathway, which can regulate the expression of genes like MuRF1, FOXO1, Atrogin 1, and other ligases that are essential members of the ubiquitin system. On the other hand, PACAP stimulates the secretion of CRH in response to stress, activating the ubiquitin signaling pathway that plays a vital role in protein degradation and regulates oxidative stress and immune responses. Many studies conducted on rodents, mammals, and other models confirm the regulatory effects of PACAP, cAMP, and the ubiquitin pathway; however, there are no studies testing whether PACAP-induced cAMP signaling in poultry regulates the ubiquitin pathway. Besides, it would be interesting to investigate if PACAP can regulate ubiquitin signaling during stress response via CRH altered by HPA axis stimulation. Therefore, this review highlights a summary of research studies that indicate the potential interaction of the PACAP and ubiquitin signaling pathways on different molecular and physiological parameters in poultry species through the cAMP and stress signaling pathways.

Review: The role of heat shock proteins in chicken: Insights into stress adaptation and health

This review article aimed to provide readers with a comprehensive understanding of the function of heat shock proteins (HSPs) in chicken physiology, stress response, and overall poultry health. With the increasing challenges faced by the livestock industry, particularly the poultry sector, due to climate change-induced high ambient temperatures, heat stress (HS) has become a critical concern. HS disrupts the thermal balance in poultry, leading to detrimental effects on growth, immune function, and overall health. HSPs play a pivotal role in mitigating the impacts of HS in chickens. These molecular chaperones are involved in protein folding, unfolding, and assembly, and they are classified into several families based on their size, including small molecule HSPs, HSP40, HSP60, HSP70, HSP90, and HSP110. By maintaining cellular homeostasis and promoting stress tolerance, HSPs act as vital guardians in helping chickens cope with HS and its associated consequences. The review synthesized relevant literature to shed light on the importance of HSPs in stress adaptation, cellular homeostasis, and the maintenance of normal cell metabolism in chickens. The adverse effects of HS on chickens include oxidative stress and compromised immune systems, making them more susceptible to infections. So also, HS negatively affects production performance and meat quality in poultry. Understanding the functions of HSPs in chickens offers valuable insights into stress adaptation and health, and could potentially lead to the identification of HSP biomarkers, genetic selection for heat tolerance, investigations into the interplay between HSPs and immune function, and the development of nutritional interventions to enhance HSP activity. By exploring these potential research directions, the review aimed to contribute to the development of novel approaches to mitigate the negative effects of HS on poultry, ultimately improving productivity and animal welfare in a changing climate.

Identification of Novel mRNA Isoforms Associated with Acute Heat Stress Response Using RNA Sequencing Data in Sprague Dawley Rats

The molecular mechanisms underlying heat stress tolerance in animals to high temperatures remain unclear. This study identified the differentially expressed mRNA isoforms which narrowed down the most reliable DEG markers and molecular pathways that underlie the mechanisms of thermoregulation. This experiment was performed on Sprague Dawley rats housed at 22 °C (control group; CT), and three acute heat-stressed groups housed at 42 °C for 30 min (H30), 60 min (H60), and 120 min (H120). Earlier, we demonstrated that acute heat stress increased the rectal temperature of rats, caused abnormal changes in the blood biochemical parameters, as well as induced dramatic changes in the expression levels of genes through epigenetics and post-transcriptional regulation. Transcriptomic analysis using RNA-Sequencing (RNA-Seq) data obtained previously from blood (CT and H120), liver (CT, H30, H60, and H120), and adrenal glands (CT, H30, H60, and H120) was performed. The differentially expressed mRNA isoforms (DEIs) were identified and annotated by the CLC Genomics Workbench. Biological process and metabolic pathway analyses were performed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. A total of 225, 5764, and 4988 DEIs in the blood, liver, and adrenal glands were observed. Furthermore, the number of novel differentially expressed transcript lengths with annotated genes and novel differentially expressed transcript with non-annotated genes were 136 and 8 in blood, 3549 and 120 in the liver, as well as 3078 and 220 in adrenal glands, respectively. About 35 genes were involved in the heat stress response, out of which, Dnaja1, LOC680121, Chordc1, AABR07011951.1, Hsp90aa1, Hspa1b, Cdkn1a, Hmox1, Bag3, and Dnaja4 were commonly identified in the liver and adrenal glands, suggesting that these genes may regulate heat stress response through interactions between the liver and adrenal glands. In conclusion, this study would enhance our understanding of the complex underlying mechanisms of acute heat stress, and the identified mRNA isoforms and genes can be used as potential candidates for thermotolerance selection in mammals.

Label-free quantitative proteomics and stress responses in pigs-The case of short or long road transportation

Ethical livestock production is currently a major concern for consumers. In parallel, research has shown that transport duration is an important factor affecting animal welfare and has a negative impact on the final product quality and on the production cost. This study applied proteomics methods to the animal stress/welfare problem in pigs muscle-exudate with the aim to identify proteins indicative of molecular processes underpinning transport stress and to better characterise this species as a biomedical model. A broader perspective of the problem was obtained by applying label-free LC-MS to characterise the proteome response to transport stress (short or long road transportation) in pigs within the same genetic line. A total of 1,464 proteins were identified, following statistical analysis 66 proteins clearly separating pigs subject to short road transportation and pigs subject long road transportation. These proteins were mainly involved in cellular and metabolic processes. Catalase and stress-induced phosphoprotein-1 were further confirmed by Western blot as being involved in the process of self-protection of the cells in response to stress. This study provide an insight into the molecular processes that are involved in pig adaptability to transport stress and are a step-forward for the development of an objective evaluation method of stress in order to improve animal care and management in farm animals.

Climate change and heat stress: Impact on production, reproduction and growth performance of poultry and its mitigation using genetic strategies

Heat stress is an important environmental determinant which adversely affects the performance of poultry worldwide. The present communication reviews the impact of heat stress on production, reproduction and growth performance of poultry, and its alleviation using genetic strategies. The adverse effects of high environmental temperature on poultry include decrease in growth rate, body weight, egg production, egg weight, egg quality, meat quality, semen quality, fertility and hatchability, which cause vast financial losses to the poultry industry. High ambient temperature has an antagonistic effect on performance traits of the poultry. Thus, selection of birds for high performance has increased their susceptibility to heat stress. Additionally, heat burden during transportation of birds from one place to another leads to reduced meat quality, increased mortality and welfare issues. Molecular markers are being explored nowadays to recognize the potential candidate genes related to production, reproduction and growth traits for selecting poultry birds to enhance thermo-tolerance and resistance against diseases. In conclusion, there is a critical need of formulating selection strategies based on genetic markers and exploring more genes in addition to HSP25, 70, 90, H1, RB1CC, BAG3, PDK, ID1, Na, F, dw and K responsible for thermoregulation, to improve the overall performance of poultry along with their ability to tolerate heat stress conditions.

Emerging Genetic Tools to Investigate Molecular Pathways Related to Heat Stress in Chickens: A Review

Simple Summary

New genomic tools have been used as an instrument in order to assess the molecular pathway involved in heat stress resistance. Local chicken breeds have a better attitude to face heat stress. This review aims to summarize studies linked to chickens, heat stress, and heat shock protein.

Abstract

Chicken products are the most consumed animal-sourced foods at a global level across greatly diverse cultures, traditions, and religions. The consumption of chicken meat has increased rapidly in the past few decades and chicken meat is the main animal protein source in developing countries. Heat stress is one of the environmental factors which decreases the productive performance of poultry and meat quality. Heat stress produces the over-expression of heat shock factors and heat shock proteins in chicken tissues. Heat shock proteins regulate several molecular pathways in cells in response to stress conditions, changing the homeostasis of cells and tissues. These changes can affect the physiology of the tissue and hence the production ability of chickens. Indeed, commercial chicken strains can reach a high production level, but their body metabolism, being comparatively accelerated, has poor thermoregulation. In contrast, native backyard chickens are more adapted to the environments in which they live, with a robustness that allows them to survive and reproduce constantly. In the past few years, new molecular tools have been developed, such as RNA-Seq, Single Nucleotide Polymorphisms (SNPs), and bioinformatics approaches such as Genome-Wide Association Study (GWAS). Based on these genetic tools, many studies have detected the main pathways involved in cellular response mechanisms. In this context, it is necessary to clarify all the genetic and molecular mechanisms involved in heat stress response. Hence, this paper aims to review the ability of the new generation of genetic tools to clarify the molecular pathways associated with heat stress in chickens, offering new perspectives for the use of these findings in the animal breeding field.

Effect of chronic and acute heat challenges on fecal microbiota composition, production, and thermoregulation traits in growing pigs1,2

The present study aimed at investigating the impact of heat challenges on gut microbiota composition in growing pigs and its relationship with pigs’ performance and thermoregulation responses. From a total of 10 F1 sire families, 558 and 564 backcross Large White × Créole pigs were raised and phenotyped from 11 to 23 wk of age in temperate (TEMP) and in tropical (TROP) climates, respectively. In TEMP, all pigs were subjected to an acute heat challenge (3 wk at 29 °C) from 23 to 26 wk of age. Feces samples were collected at 23 wk of age both in TEMP and TROP climate (TEMP23 and TROP23 samples, respectively) and at 26 wk of age in TEMP climate (TEMP26 samples) for 16S rRNA analyses of fecal microbiota composition. The fecal microbiota composition significantly differed between the 3 environments. Using a generalized linear model on microbiota composition, 182 operational taxonomic units (OTU) and 2 pathways were differentially abundant between TEMP23 and TEMP26, and 1,296 OTU and 20 pathways between TEMP23 and TROP23. Using fecal samples collected at 23 wk of age, pigs raised under the 2 climates were discriminated with 36 OTU using a sparse partial least square discriminant analysis that had a mean classification error-rate of 1.7%. In contrast, pigs in TEMP before the acute heat challenge could be discriminated from the pigs in TEMP after the heat challenge with 32 OTU and 9.3% error rate. The microbiota can be used as biomarker of heat stress exposition. Microbiota composition revealed that pigs were separated into 2 enterotypes. The enterotypes were represented in both climates. Whatever the climate, animals belonging to the Turicibacter–Sarcina–Clostridium sensu stricto dominated enterotype were 3.3 kg heavier (P < 0.05) at 11 wk of age than those belonging to the Lactobacillus-dominated enterotype. This latter enterotype was related to a 0.3 °C lower skin temperature (P < 0.05) at 23 wk of age. Following the acute heat challenge in TEMP, this enterotype had a less-stable rectal temperature (0.34 vs. 0.25 °C variation between weeks 23 and 24, P < 0.05) without affecting growth performance (P > 0.05). Instability of the enterotypes was observed in 34% of the pigs, switching from an enterotype to another between 23 and 26 wk of age after heat stress. Despite a lower microbial diversity, the Turicibacter–Sarcina–Clostridium sensu stricto dominated enterotype was better adapted to heat stress conditions with lower thermoregulation variations.

Effects of duration of thermal stress on growth performance, serum oxidative stress indices, the expression and localization of ABCG2 and mitochondria ROS production of skeletal muscle, small intestine and immune organs in broilers

The purpose of the current study was to investigate that effect of duration of thermal stress on growth performance, oxidative stress indices in serum, the expression and localization of ABCG2, and mitochondria ROS production in skeletal muscle, small intestine and immune organs, and then to further reveal correlations between indicators. At 28 days of age, sixty broilers were randomly divided into the control group (25 ± 2 °C; 24 h/day) and the heat stress group (36 ± 2 °C; 8 h/day lasted for 1 week or 2 weeks). Fifteen broilers per group were respectively euthanized, and some samples were respectively collected from the control and the heat stress groups at the end of the 1st week or the 2nd week of heat stress. A typical heat stress response has been observed at this temperature. Compared with the control group, the birds subjected to heat stress at the end of the 1st week reduced (P ＜ 0.05) body weight (BW), average daily feed intake (ADFI), average daily gain (ADG), the activity of serum antioxidant enzyme and content of glutathione (GSH), while increased (P ＜ 0.05) feed conversion ratio (FCR), serum corticosterone and malondialdehyde (MDA) levels. However, when the heat stress lasted for the end of the 2nd week, there was no significant difference (P ＞ 0.05) in ADFI, ADG, FCR and serum contents of corticosterone, MDA and GSH. Regardless of duration of thermal stress, the localization of ABCG2 protein had no change. Moreover, heat stress also did not affect (P ＞ 0.05) the IOD of the ABCG2 positive portion and the expression of the ABCG2 mRNA in the pectorales, crureus, duodenum, jejunum, ileum and spleen, while significantly increased (P ＜ 0.05) the corresponding tissues ROS production at the end of the 1st week of heat stress. In contrast, at the end of the 2nd week of heat stress, IOD of the ABCG2 positive portion and the expression of the ABCG2 mRNA in heat stress group significantly increased (P ＜ 0.05), while the corresponding tissues ROS production had no difference (P ＞ 0.05) compared to the control group. Collectively, duration of thermal stress affects growth performance, serum oxidative stress indices, and the expression of ABCG2 and the ROS production of broiler tissues in a time-dependent manner. There is a negative correlation between the expression of ABCG2 and the ROS production in the corresponding tissues under heat stress.

Transcriptomic profiles of muscle, heart, and spleen in reaction to circadian heat stress in Ethiopian highland and lowland male chicken

Temperature stress impacts both welfare and productivity of livestock. Global warming is expected to increase the impact, especially in tropical areas. We investigated the biological mechanisms regulated by temperature stress due to the circadian temperature cycle in temperature adapted and non-adapted chicken under tropical conditions. We studied transcriptome profiles of heart, breast muscle, and spleen tissues of Ethiopian lowland chicken adapted to high circadian temperatures and non-adapted Ethiopian highland chicken under lowland conditions at three points during the day: morning, noon, and evening. Functional annotations and network analyses of genes differentially expressed among the time points of the day indicate major differences in the reactions of the tissues to increasing and decreasing temperatures, and also the two chickens lines differ. However, epigenetic changes of chromatin methylation and histone (de)acetylation seemed to be central regulatory mechanisms in all tissues in both chicken lines. Finally, all tissues showed differentially expressed genes between morning and evening times indicating biological mechanisms that need to change during the night to reach morning levels again the next day.

Acute Heat Stress Changes Protein Expression in the Testes of a Broiler-Type Strain of Taiwan Country Chickens

Heat stress leads to decreased fertility in roosters. This study investigated the global protein expression in response to acute heat stress in the testes of a broiler-type strain of Taiwan country chickens (TCCs). Twelve 45-week-old roosters were randomly allocated to the control group maintained at 25°C, and three groups subjected to acute heat stress at 38°C for 4 h, with 0, 2, and 6 h of recovery, respectively. Testis samples were collected for hematoxylin and eosin staining, apoptosis assay, and protein analysis. The results revealed 101 protein spots that differed significantly from the control following exposure to acute heat stress. The proteins that were differentially expressed participated mainly in protein metabolism and other metabolic processes, responses to stimuli, apoptosis, cellular organization, and spermatogenesis. Proteins that negatively regulate apoptosis were downregulated and proteins involved in autophagy and major heat shock proteins (HSP90α, HSPA5, and HSPA8) were upregulated in the testes of heat-stressed chickens. In conclusion, acute heat stress causes a change in protein expression in the testes of broiler-type B strain TCCs and may thus impair cell morphology, spermatogenesis, and apoptosis. The expression of heat shock proteins increased to attenuate the testicular injury induced by acute heat stress.

Acute phase protein mRNA expressions and enhancement of antioxidant defense system in Black-meated Silkie Fowls supplemented with clove (Eugenia caryophyllus) extracts under the influence of chronic heat stress

Background

The current study investigates the anti-stress effects of clove (Eugenia caryophyllus) extracts (0, 200, 400, and 600 mg/kg) on serum antioxidant biomarkers, immune response, immunological organ growth index, and expression levels of acute phase proteins (APPs); ovotransferrin (OVT), ceruloplasmin (CP), ceruloplasmin (AGP), C-reactive protein (CRP), and serum amyloid-A (SAA) mRNA in the immunological organs of 63-d-old male black-meated Silkie fowls subjected to 21 d chronic heat stress at 35 ± 2 °C.

Results

The results demonstrated that clove extract supplementation in the diet of Silkie fowls subjected to elevated temperature (ET) improve growth performance, immune responses, and suppressed the activities of glutathion peroxidase (GSH-Px), superoxide dismutase (SOD), catalase (CAT), and thioredoxin reductase (TXNRD); reduced serum malonaldehyde (MDA) and glutathione (GSH) concentrations when compared with fowls raised under thermoneutral condition (TC). Upon chronic heat stress and supplementation of clove extracts, the Silkie fowls showed a linear increase in GSH-Px, SOD, CAT, and TXNRD activities (P = 0.01) compared with fowls fed diets without clove extract. ET decreased (P < 0.05) the growth index of the liver, spleen, bursa of Fabricius and thymus. However, the growth index of the liver, spleen, bursa of Fabricius and thymus increased significantly (P < 0.05) which corresponded to an increase in clove supplemented levels. The expression of OVT, CP, AGP, CRP, and SAA mRNA in the liver, spleen, bursa of Fabricius and thymus were elevated (P < 0.01) by ET compared with those maintained at TC. Nevertheless, clove mitigates heat stress-induced overexpression of OVT, CP, AGP, CRP and SAA mRNA in the immune organs of fowls fed 400 mg clove/kg compared to other groups.

Conclusions

The results showed that clove extracts supplementation decreased oxidative stress in the heat-stressed black-meated fowls by alleviating negative effects of heat stress via improvement in growth performance, antioxidant defense mechanisms, immunity, and regulate the expression of acute phase genes in the liver and immunological organs.

Electronic supplementary material

The online version of this article (doi:10.1186/s40781-016-0122-4) contains supplementary material, which is available to authorized users.

Heat Stress and Lipopolysaccharide Stimulation of Chicken Macrophage-Like Cell Line Activates Expression of Distinct Sets of Genes

Acute heat stress requires immediate adjustment of the stressed individual to sudden changes of ambient temperatures. Chickens are particularly sensitive to heat stress due to development of insufficient physiological mechanisms to mitigate its effects. One of the symptoms of heat stress is endotoxemia that results from release of the lipopolysaccharide (LPS) from the guts. Heat-related cytotoxicity is mitigated by the innate immune system, which is comprised mostly of phagocytic cells such as monocytes and macrophages. The objective of this study was to analyze the molecular responses of the chicken macrophage-like HD11 cell line to combined heat stress and lipopolysaccharide treatment in vitro. The cells were heat-stressed and then allowed a temperature-recovery period, during which the gene expression was investigated. LPS was added to the cells to mimic the heat-stress-related endotoxemia. Semi high-throughput gene expression analysis was used to study a gene panel comprised of heat shock proteins, stress-related genes, signaling molecules and immune response genes. HD11 cell line responded to heat stress with increased mRNA abundance of the HSP25, HSPA2 and HSPH1 chaperones as well as DNAJA4 and DNAJB6 co-chaperones. The anti-apoptotic gene BAG3 was also highly up-regulated, providing evidence that the cells expressed pro-survival processes. The immune response of the HD11 cell line to LPS in the heat stress environment (up-regulation of CCL4, CCL5, IL1B, IL8 and iNOS) was higher than in thermoneutral conditions. However, the peak in the transcriptional regulation of the immune genes was after two hours of temperature-recovery. Therefore, we propose the potential influence of the extracellular heat shock proteins not only in mitigating effects of abiotic stress but also in triggering the higher level of the immune responses. Finally, use of correlation networks for the data analysis aided in discovering subtle differences in the gene expression (i.e. the role of the CASP3 and CASP9 genes).

Genomic analysis of Ugandan and Rwandan chicken ecotypes using a 600 k genotyping array

Background

Indigenous populations of animals have developed unique adaptations to their local environments, which may include factors such as response to thermal stress, drought, pathogens and suboptimal nutrition. The survival and subsequent evolution within these local environments can be the result of both natural and artificial selection driving the acquisition of favorable traits, which over time leave genomic signatures in a population. This study’s goals are to characterize genomic diversity and identify selection signatures in chickens from equatorial Africa to identify genomic regions that may confer adaptive advantages of these ecotypes to their environments.

Results

Indigenous chickens from Uganda (n = 72) and Rwanda (n = 100), plus Kuroilers (n = 24, an Indian breed imported to Africa), were genotyped using the Axiom® 600 k Chicken Genotyping Array. Indigenous ecotypes were defined based upon location of sampling within Africa. The results revealed the presence of admixture among the Ugandan, Rwandan, and Kuroiler populations. Genes within runs of homozygosity consensus regions are linked to gene ontology (GO) terms related to lipid metabolism, immune functions and stress-mediated responses (FDR < 0.15). The genes within regions of signatures of selection are enriched for GO terms related to health and oxidative stress processes. Key genes in these regions had anti-oxidant, apoptosis, and inflammation functions.

Conclusions

The study suggests that these populations have alleles under selective pressure from their environment, which may aid in adaptation to harsh environments. The correspondence in gene ontology terms connected to stress-mediated processes across the populations could be related to the similarity of environments or an artifact of the detected admixture.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2711-5) contains supplementary material, which is available to authorized users.

Thermal manipulation of the chicken embryo triggers differential gene expression in response to a later heat challenge

Background

Meat type chickens have limited capacities to cope with high environmental temperatures, this sometimes leading to mortality on farms and subsequent economic losses. A strategy to alleviate this problem is to enhance adaptive capacities to face heat exposure using thermal manipulation (TM) during embryogenesis. This strategy was shown to improve thermotolerance during their life span. The aim of this study was to determine the effects of TM (39.5 °C, 12 h/24 vs 37.8 °C from d7 to d16 of embryogenesis) and of a subsequent heat challenge (32 °C for 5 h) applied on d34 on gene expression in the Pectoralis major muscle (PM). A chicken gene expression microarray (8 × 60 K) was used to compare muscle gene expression profiles of Control (C characterized by relatively high body temperatures, Tb) and TM chickens (characterized by a relatively low Tb) reared at 21 °C and at 32 °C (CHC and TMHC, respectively) in a dye-swap design with four comparisons and 8 broilers per treatment. Real-time quantitative PCR (RT-qPCR) was subsequently performed to validate differential expression in each comparison. Gene ontology, clustering and network building strategies were then used to identify pathways affected by TM and heat challenge.

Results

Among the genes differentially expressed (DE) in the PM (1.5 % of total probes), 28 were found to be differentially expressed between C and TM, 128 between CHC and C, and 759 between TMHC and TM. No DE gene was found between TMHC and CHC broilers. The majority of DE genes analyzed by RT-qPCR were validated. In the TM/C comparison, DE genes were involved in energy metabolism and mitochondrial function, cell proliferation, vascularization and muscle growth; when comparing heat-exposed chickens to their own controls, TM broilers developed more specific pathways than C, especially involving genes related to metabolism, stress response, vascularization, anti-apoptotic and epigenetic processes.

Conclusions

This study improved the understanding of the long-term effects of TM on PM muscle. TM broilers displaying low Tb may have lower metabolic intensity in the muscle, resulting in decreased metabolic heat production, whereas modifications in vascularization may enhance heat loss. These specific changes could in part explain the better adaptation of TM broilers to heat.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2661-y) contains supplementary material, which is available to authorized users.

Annotation of Differential Gene Expression in Small Yellow Follicles of a Broiler-Type Strain of Taiwan Country Chickens in Response to Acute Heat Stress

This study investigated global gene expression in the small yellow follicles (6-8 mm diameter) of broiler-type B strain Taiwan country chickens (TCCs) in response to acute heat stress. Twelve 30-wk-old TCC hens were divided into four groups: control hens maintained at 25°C and hens subjected to 38°C acute heat stress for 2 h without recovery (H2R0), with 2-h recovery (H2R2), and with 6-h recovery (H2R6). Small yellow follicles were collected for RNA isolation and microarray analysis at the end of each time point. Results showed that 69, 51, and 76 genes were upregulated and 58, 15, 56 genes were downregulated after heat treatment of H2R0, H2R2, and H2R6, respectively, using a cutoff value of two-fold or higher. Gene ontology analysis revealed that these differentially expressed genes are associated with the biological processes of cell communication, developmental process, protein metabolic process, immune system process, and response to stimuli. Upregulation of heat shock protein 25, interleukin 6, metallopeptidase 1, and metalloproteinase 13, and downregulation of type II alpha 1 collagen, discoidin domain receptor tyrosine kinase 2, and Kruppel-like factor 2 suggested that acute heat stress induces proteolytic disintegration of the structural matrix and inflamed damage and adaptive responses of gene expression in the follicle cells. These suggestions were validated through gene expression, using quantitative real-time polymerase chain reaction. Functional annotation clarified that interleukin 6-related pathways play a critical role in regulating acute heat stress responses in the small yellow follicles of TCC hens.

Transcriptome response to heat stress in a chicken hepatocellular carcinoma cell line

Heat stress triggers an evolutionarily conserved set of responses in cells. The transcriptome responds to hyperthermia by altering expression of genes to adapt the cell or organism to survive the heat challenge. RNA-seq technology allows rapid identification of environmentally responsive genes on a large scale. In this study, we have used RNA-seq to identify heat stress responsive genes in the chicken male white leghorn hepatocellular (LMH) cell line. The transcripts of 812 genes were responsive to heat stress (p < 0.01) with 235 genes upregulated and 577 downregulated following 2.5 h of heat stress. Among the upregulated were genes whose products function as chaperones, along with genes affecting collagen synthesis and deposition, transcription factors, chromatin remodelers, and genes modulating the WNT and TGF-beta pathways. Predominant among the downregulated genes were ones that affect DNA replication and repair along with chromosomal segregation. Many of the genes identified in this study have not been previously implicated in the heat stress response. These data extend our understanding of the transcriptome response to heat stress with many of the identified biological processes and pathways likely to function in adapting cells and organisms to hyperthermic stress. Furthermore, this study should provide important insight to future efforts attempting to improve species abilities to withstand heat stress through genome-wide association studies and breeding.

Label-free Quantitative Analysis of Changes in Broiler Liver Proteins under Heat Stress using SWATH-MS Technology

High temperature is one of the key environmental stressors affecting broiler production efficiency and meat yield. Knowledge of broiler self-regulation mechanisms under heat stress is important for the modern scale of poultry breeding. In the present study, the SWATH strategy was employed to investigate the temporal response of the broiler liver to heat stress. A total of 4,271 proteins were identified and used to generate a reference library for SWATH analysis. During this analysis, 2,377 proteins were quantified, with a coefficient of variation ≤25% among technical and biological replicates. A total of 257 proteins showed differential expression between the control and heat stressed groups. Consistent results for 26 and 5 differential proteins were validated respectively by MRM and western blotting quantitative analyses. Bioinformatics analysis suggests that the up- and down-regulation of these proteins appear involved in the following three categories of cellular pathways and metabolisms: 1) inhibit the ERK signaling pathway; 2) affect broiler liver lipid and amino acid metabolism; 3) induce liver cell immune responses to adapt to the high temperatures and reduce mortality. The study reported here provides an insight into broiler self-regulation mechanisms and shed light on the improved broiler adaptability to high-temperature environments.

Profiling of differential gene expression in the hypothalamus of broiler-type Taiwan country chickens in response to acute heat stress

Acute heat stress severely impacts poultry production. The hypothalamus acts as a crucial center to regulate body temperature, detect temperature changes, and modulate the autonomic nervous system and endocrine loop for heat retention and dissipation. The purpose of this study was to investigate global gene expression in the hypothalamus of broiler-type B strain Taiwan country chickens after acute heat stress. Twelve 30-week-old hens were allocated to four groups. Three heat-stressed groups were subjected to acute heat stress at 38 °C for 2 hours without recovery (H2R0), with 2 hours of recovery (H2R2), and with 6 hours of recovery (H2R6). The control hens were maintained at 25 °C. At the end, hypothalamus samples were collected for gene expression analysis. The results showed that 24, 11, and 25 genes were upregulated and 41, 15, and 42 genes were downregulated in H2R0, H2R2, and H2R6 treatments, respectively. The expressions of gonadotropin-releasing hormone 1 (GNRH1), heat shock 27-kDa protein 1 (HSPB1), neuropeptide Y (NPY), and heat shock protein 25 (HSP25) were upregulated at all recovery times after heat exposure. Conversely, the expression of TPH2 was downregulated at all recovery times. A gene ontology analysis showed that most of the differentially expressed genes were involved in biological processes including cellular processes, metabolic processes, localization, multicellular organismal processes, developmental processes, and biological regulation. A functional annotation analysis showed that the differentially expressed genes were related to the gene networks of responses to stress and reproductive functions. These differentially expressed genes might be essential and unique key factors in the heat stress response of the hypothalamus in chickens.

Transcriptome responses to heat stress in hypothalamus of a meat-type chicken

Background

Heat stress has resulted in great losses in poultry production. To address this issue, we systematically analyzed chicken hypothalamus transcriptome responses to thermal stress using a 44 k chicken Agilent microarray,

Methods

Hypothalamus samples were collected from a control group reared at 25°C, a heat-stress group treated at 34°C for 24 h, and a temperature-recovery group reared at 25°C for 24 h following a heat-stress treatment. We compared the expression profiles between each pair of the three groups using microarray data.

Results

A total of 1,967 probe sets were found to be differentially expressed in the three comparisons with P < 0.05 and a fold change (FC) higher than 1.5, and the genes were mainly involved in self-regulation and compensation required to maintain homeostasis. Consistent expression results were found for 11 selected genes by quantitative real-time PCR. Thirty-eight interesting differential expression genes were found from GO term annotation and those genes were related to meat quality, growth, and crucial enzymes. Using these genes for genetic network analysis, we obtained three genetic networks. Moreover, the transcripts of heat-shock protein, including Hsp 40 and Hsp 90, were significantly altered in response to thermal stress.

Conclusions

This study provides a broader understanding of molecular mechanisms underlying stress response in chickens and discovery of novel genes that are regulated in a specific thermal-stress manner.

Electronic supplementary material

The online version of this article (doi:10.1186/s40104-015-0003-6) contains supplementary material, which is available to authorized users.

RNA-seq analysis of broiler liver transcriptome reveals novel responses to high ambient temperature

BACKGROUND

In broilers, high ambient temperature can result in reduced feed consumption, digestive inefficiency, impaired metabolism, and even death. The broiler sector of the U.S. poultry industry incurs approximately $52 million in heat-related losses annually. The objective of this study is to characterize the effects of cyclic high ambient temperature on the transcriptome of a metabolically active organ, the liver. This study provides novel insight into the effects of high ambient temperature on metabolism in broilers, because it is the first reported RNA-seq study to characterize the effect of heat on the transcriptome of a metabolic-related tissue. This information provides a platform for future investigations to further elucidate physiologic responses to high ambient temperature and seek methods to ameliorate the negative impacts of heat.

RESULTS

Transcriptome sequencing of the livers of 8 broiler males using Illumina HiSeq 2000 technology resulted in 138 million, 100-base pair single end reads, yielding a total of 13.8 gigabases of sequence. Forty genes were differentially expressed at a significance level of P-value < 0.05 and a fold-change ≥ 2 in response to a week of cyclic high ambient temperature with 27 down-regulated and 13 up-regulated genes. Two gene networks were created from the function-based Ingenuity Pathway Analysis (IPA) of the differentially expressed genes: "Cell Signaling" and "Endocrine System Development and Function". The gene expression differences in the liver transcriptome of the heat-exposed broilers reflected physiological responses to decrease internal temperature, reduce hyperthermia-induced apoptosis, and promote tissue repair. Additionally, the differential gene expression revealed a physiological response to regulate the perturbed cellular calcium levels that can result from high ambient temperature exposure.

CONCLUSIONS

Exposure to cyclic high ambient temperature results in changes at the metabolic, physiologic, and cellular level that can be characterized through RNA-seq analysis of the liver transcriptome of broilers. The findings highlight specific physiologic mechanisms by which broilers reduce the effects of exposure to high ambient temperature. This information provides a foundation for future investigations into the gene networks involved in the broiler stress response and for development of strategies to ameliorate the negative impacts of heat on animal production and welfare.

Exploring the molecular mechanism of acute heat stress exposure in broiler chickens using gene expression profiling

The process of heat regulation is complex and its exact molecular mechanism is not fully understood. In this study, to investigate the global gene regulation response to acute heat exposure, gene microarrays were exploited to analyze the effects of heat stress on three tissues (brain, liver, leg muscle) of the yellow broiler chicken (Gallus gallus). We detected 166 differentially expressed genes (DEGs) in the brain, 219 in the leg muscle and 317 in the liver. Six of these genes were differentially expressed in all three tissues and were validated by qRT-PCR, and included heat shock protein genes (HSPH1, HSP25), apoptosis-related genes (RB1CC1, BAG3), a cell proliferation and differentiation-related gene (ID1) and the hunger and energy metabolism related gene (PDK). All these genes might be important factors in chickens suffering from heat stress. We constructed gene co-expression networks using the DEGs of the brain, leg muscle and liver and two, four and two gene co-expression modules were identified in these tissues, respectively. Functional enrichment of these gene modules revealed that various functional clusters were related to the effects of heat stress, including those for cytoskeleton, extracellular space, ion binding and energy metabolism. We concluded that these genes and functional clusters might be important factors in chickens under acute heat stress. Further in-depth research on the newly discovered heat-related genes and functional clusters is required to fully understand their molecular functions in thermoregulation.

Genome-wide expression analysis of roxarsone-stimulated growth of broiler chickens (Gallus gallus)

Roxarsone is a commonly used additive in chicken (Gallus gallus) industry. However, little is known on the intrinsic molecular mechanism via which the growth performance of birds improves. This study was therefore performed to investigate the expression profiles of genes induced by roxarsone. Fifty-six broiler chickens were divided into two groups, namely treated and untreated with roxarsone. The treated group was provided a diet of 45.4mg/kg roxarsone medication and the other group acted as control. Data analysis showed that roxarsone consistently and significantly (P<0.05) increased chicken growth performance. In addition to this a significant (P<0.05) increase of arsenic residue in liver has been seen. Microarray expression analysis of 8935 genes in liver showed that 22 genes (10 up- and 12 down-regulated) had altered expression throughout the experimental periods. Two novel genes (GenBank accession no. GU724343 and GU724344) were cloned through rapid amplification of cDNA ends (RACE). Gene GU724343 was predicted to encode an unidentified protein and the second gene GU724344 was presumed to encode a new member of immunoglobulin-like receptor (CHIR) family. Our results suggested for the first time that the role of roxarsone could be mainly to modify the expression levels of cell growth, immunity/defense and energy metabolism associated genes, as a result promoting animal growth. Further research on these genes should help to increase the knowledge of improving animal productivity safely and effectively.